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vep_id_batch

Batch annotate multiple variant identifiers (rs, COSM, etc.) to retrieve functional consequences, conservation scores, and pathogenicity predictions from Ensembl VEP.

Instructions

Annotate multiple variants using identifiers in batch

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
speciesYesSpecies name (e.g., 'homo_sapiens', 'mus_musculus')homo_sapiens
variant_idsYesList of variant identifiers (e.g., ['rs56116432', 'COSM476'])
canonicalNoInclude only canonical transcripts per gene
hgvsNoInclude HGVS nomenclature
domainsNoInclude protein domain information
ccdsNoInclude CCDS transcript identifiers
proteinNoInclude protein sequence identifiers
AlphaMissenseNoInclude AlphaMissense pathogenicity scores
CADDNoInclude CADD deleteriousness scores
REVELNoInclude REVEL pathogenicity scores
ConservationNoInclude conservation scores
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full burden of behavioral disclosure. It only states the basic function and does not mention whether the operation is read-only, if there are rate limits, batch size constraints, or how invalid identifiers are handled. The agent lacks critical safety and constraint information.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single, well-structured sentence that efficiently conveys the core purpose. It is front-loaded with the key verb and resource. There is no wasted text, though it could benefit from slightly more detail given the tool's complexity.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given 11 parameters and no output schema, the description is too brief. It does not explain the return format, how to interpret results, or error scenarios. While the sibling tools are listed, no contextual hints (e.g., typical use cases) are provided. The description leaves significant gaps for an agent.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the baseline is 3. The description adds no additional meaning beyond the schema; it does not elaborate on parameter usage, defaults, or interdependencies. However, the schema itself is self-explanatory, so the description does not detract.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's action ('Annotate'), resource ('multiple variants'), and method ('using identifiers in batch'). It distinguishes from siblings like 'vep_id_single' (single variant) and 'vep_hgvs_batch' (HGVS-based), though it doesn't explicitly name the identifier types (e.g., rs, COSM) which are in the schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No guidance is provided on when to use this tool versus alternatives. It does not mention that it is for multiple variant IDs, nor does it direct users to 'vep_id_single' for single variants or to 'vep_hgvs_batch' for HGVS notation. The purpose is implicit from the tool name and sibling list but not explicit in the description.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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